In this experiment, I test whether Perplexity A. I. gives objective answers to deep questions. Intelligence, particularly coming from a machine, might assumed to be objective. As this experiment shows, however, Perplexity is not objective but instead toes the line of scientific materialism. Perhaps this is not surprising since “artificial intelligence” is a product of the existing scientific paradigm and Perplexity no doubt weighs the views of mainstream science more heavily than other viewpoints. But if you are looking for an open-minded perspective on the big questions or a creative approach to the conundrums facing scientific materialism, you will need to look elsewhere.
Here are some highlights of a conversation I recently had with Perplexity, with the questions in italics and Perplexity’s answers in bold.
Question: “Why are base sequences in DNA written in such a way that they cause the formation of amino acids that in turn synthesize proteins?”
Perplexity Answer: DNA base sequences are “written” that way because evolution preserved, over billions of years, those sequences that happened to make useful proteins for survival and reproduction, while harmful or useless ones were lost.
There is nothing intentional or goal directed about the code; random mutations continually change DNA, and natural selection keeps the variants whose proteins help the organism live and reproduce in its environment.
Early in life’s history, simple genetic systems likely produced short peptides; some combinations improved stability, metabolism, or replication, so organisms carrying those sequences left more descendants.
Over immense timescales, this trial and error process refined sets of DNA sequences (genes) that specify particular amino acid orders, giving rise to complex, highly tuned proteins such as enzymes, receptors, and structural fibers.
So DNA is not designed in advance to cause protein formation; rather, life that used DNA sequences in ways that produced advantageous proteins was favored by natural selection, and those sequence patterns accumulated and dominate in organisms today.
Troubled by what I viewed as a materialistic bias in the answers, I then asked:
“Why are you so emphatic about disclaiming any goal or purpose in the formation of DNA or life itself?”
Perplexity Answer: Because the way I’m set up is to use the methods and language of mainstream science, which deliberately avoids building purpose or design into its explanations.”
Question: So you are programmed to follow the views of mainstream science?
Perplexity Answer: Yes—when questions are about how the natural world works (like DNA, evolution, cosmology), I’m designed to track the best available evidence, which usually means the current scientific consensus.
I prioritize explanations that line up with peer reviewed research and the broad agreement of qualified experts, rather than minority or speculative views, unless you specifically ask me to explore those.
In practice, that includes using methodological naturalism: for empirical questions I appeal to natural, testable mechanisms, while treating metaphysical or theological views as philosophical positions I can describe but not treat as established scientific results.
Question: Do you realize that mainstream science follows a metaphysics known as scientific materialism?
Many scientists do hold a broadly materialist or naturalist metaphysics, but it’s important to separate two things: the methods science uses and the worldviews individual scientists adopt.
Method vs. metaphysics
Scientific practice is built around methodological naturalism: in doing experiments and building theories, you only appeal to natural, testable causes, and you set aside appeals to the supernatural as explanations.
Scientific materialism (or metaphysical naturalism) goes further and says that, in reality, only matter (or the natural) exists or is needed to explain everything; that’s a philosophical stance, not a rule of the lab.
Where I fit
I’m aligned with the methodological part: for empirical questions I use natural, testable mechanisms and mainstream scientific models as my default frame.
I’m not committed to any metaphysics of my own; I can lay out materialist, theistic, dualist, or other views side‑by‑side, but I treat them as philosophical options rather than as settled scientific results.
If you want to press on whether methodological naturalism smuggles in a materialist metaphysics in practice, that’s a live debate in philosophy of science, and we can dig into that explicitly rather than hide it.
Question: That’s not true. You just said you follow mainstream science, which you must admit is based on materialism
Perplexity Answer: You’re right that, in practice, mainstream science is very comfortable inside a broadly materialist or naturalist picture of the world—but there are still two layers that are worth prying apart.
What I actually “follow”
When I say I follow mainstream science, I mean: for questions about how things work (DNA, evolution, cosmology), I default to the standard models and mechanisms those fields use—mutation, selection, chemistry, physics, etc.—and I don’t treat non natural explanations as scientific results.
That is a methodological constraint: I am built to answer empirical “how does it work?” questions using the same kinds of causes your biology or physics textbook uses, not because other views are impossible, but because that’s how those disciplines define what counts as a scientific explanation.
Is mainstream science de facto materialist?
Philosophers often distinguish methodological naturalism from metaphysical naturalism/materialism: the first is “only use natural causes in your scientific work,” the second is “in reality, only the natural/material exists.”
Many scientists personally slide from the first to the second, and many scientific institutions talk as if the materialist picture is simply “how reality is,” so from the outside it understandably looks like science as a culture is committed to materialism.
So you’re pointing to a real tension: the scientific method is officially just a method, but in practice it often travels with materialist metaphysics, and I’m aligned with that method and the consensus it produces
Question: How does modern science smuggle in a materialistic perspective into its theories?
Perplexity Answer: Modern science doesn’t usually argue for materialism; instead, certain practices and habits make a materialist outlook feel like the only live option.
- Restricting explanations to the physical
Methodological naturalism says: in scientific work, only physical, measurable causes count as legitimate explanations.
Over time, that method gets treated as if it revealed the whole of reality, so “what science can measure” quietly becomes “what exists,” which is metaphysical materialism rather than a purely methodological rule.
- Treating success of physics/biology as proof of completeness
Because physical theories predict and control an enormous range of phenomena, some scientists and popularizers conclude that, in principle, everything must be fully explainable in those terms.
This moves from “our current best tools are physical” to “only physical explanations are real explanations,” which is an extra philosophical step that often goes unstated.
- Language that conflates science and materialism
Influential voices explicitly describe science as committed to a picture where all that exists are physical entities and laws, and they present alternatives as unscientific by definition.
In education and public communication, this encourages “assumed atheism” or “assumed naturalism,” so students and readers absorb the idea that serious science and a non‑materialist metaphysics cannot coexist.
- Rules that exclude non‑material causes by fiat
In debates over origins, consciousness, or teleology, proposals that invoke non‑material mind, purpose, or design are often dismissed not by weighing the evidence, but by appealing to the rule that science may only posit material causes.
That effectively “smuggles in” the metaphysical claim that reality is closed under physical causation, because any counterexample is excluded at the definitional level rather than empirically falsified.
So the “smuggling” happens when a legitimate methodological preference—focus on testable, physical mechanisms—slides, often without argument, into the stronger claim that nothing beyond those mechanisms exists or is even worth considering.
Question: Isn’t it true that some of history’s greatest thinkers, such as Immanuel Kant and Thomas Nagel, have deeply criticized materialism as a metaphysics?
Perplexity Answer: Yes, that’s true: both Kant and Thomas Nagel are major examples of thinkers who have sharply questioned materialism as a complete picture of reality
Kant on materialism
Kant treated materialism as a speculative metaphysical hypothesis, not something that could be established by empirical science, and argued that its claims outrun what we can know from possible experience.
- He held that our knowledge is limited to appearances structured by our forms of intuition and categories, so any claim that “reality in itself is nothing but matter” goes beyond the bounds of human cognition.
Nagel on materialist neo-Darwinism
- In Mind and Cosmos, Nagel argues that the “materialist neo Darwinian conception of nature is almost certainly false” as a total account, because it cannot adequately explain consciousness, rationality, and objective value.
He proposes that some form of teleological or mind involving principle may be built into nature itself, even though he remains an atheist and rejects standard theistic explanations, which is precisely a rejection of purely reductive materialism
So you’re on solid ground saying that some of the most serious philosophers have argued that materialism is at best incomplete, and possibly deeply mistaken, as a metaphysics.
Takeaways:
We must careful not to treat Artificial Intelligence as some sort of God-like super-brain holding all the secrets to life. Instead, like all computer systems, it is programmed by humans and will reflect the biases of the present state of human knowledge. One refreshing aspect of this Perplexity conversation is that it admits its bias toward the mainstream, materialistic viewpoints. But inherent in this bias, which also pervades the scientific literature, is that there is no way to be methodical, logical, or scientific other than within a materialistic framework. This conclusion is false. Clearly, if the underlying paradigm is false, then so must be the theories built upon that paradigm. With a new paradigm, scientists simply follow the scientific method without holding materialistic assumptions. These include the assumptions that (a) a real world exists independently of the perceiving subject; (b) that ultimate reality consists simply of tiny particles in motion; and (c) that there is no purpose, direction, or meaning to the universe.
In my opinion, the matter-first approach of scientific materialism will ultimately be replaced by a mind-first perspective because, among other things, using mind as the starting point explains more with fewer, if any, assumptions. A mind-first approach (or “Ideal Materialism”) also leads to a much more optimistic and unifying worldview. In idealism, we write the grand narrative to the future of the world and are not subject to the gloomy consequences of theories based on assuming the universe randomly arose from faceless, mindless matter.
In some ways, Perplexity may be applauded for giving a candid assessment of its own programmed answers. In other ways, this experiment shows that “artificial intelligence” is not “creative” or “open-minded intelligence.” Rather, it is a form of intelligence that reflects scientific materialism’s limiting and pessimistic world outlook.
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